Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

The Huisgen 1,3-dipolar cycloaddition reaction of organic azides and alkynes has gained considerable attention in recent years due to the introduction in 2001 of Cu(1) catalysis by Tornoe and Meldal, leading to a major improvement in both rate and regioselectivity of the reaction, as realized independently by the Meldal and the Sharpless laboratories. The great success of the Cu(1) catalyzed reaction is rooted in the fact that it is a virtually quantitative, very robust, insensitive, general, and orthogonal ligation reaction, suitable for even biomolecular ligation and in vivo tagging or as a polymerization reaction for synthesis of long linear polymers. The triazole formed is essentially chemically inert to reactive conditions, e.g. oxidation, reduction, and hydrolysis, and has an intermediate polarity with a dipolar moment of ∼5 D. The basis for the unique properties and rate enhancement for triazole formation under Cu(1) catalysis should be found in the high ∆G of the reaction in combination with the low character of polarity of the dipole of the noncatalyzed thermal reaction, which leads to a considerable activation barrier. In order to understand the reaction in detail, it therefore seems important to spend a moment to consider the structural and mechanistic aspects of the catalysis. The reaction is quite insensitive to reaction conditions as long as Cu(1) is present and may be performed in an aqueous or organic environment both in solution and on solid support.

Cu-catalyzed azide-alkyne cycloaddition.

Controlled/living radical polymerization: Features, developments, and perspectives

Poly(ethylene glycol) (PEG) is the most used polymer and also the gold standard for stealth polymers in the emerging field of polymer-based drug delivery. The properties that account for the overwhelming use of PEG in biomedical applications are outlined in this Review. The first approved PEGylated products have already been on the market for 20 years. A vast amount of clinical experience has since been gained with this polymer--not only benefits, but possible side effects and complications have also been found. The areas that might need consideration and more intensive and careful examination can be divided into the following categories: hypersensitivity, unexpected changes in pharmacokinetic behavior, toxic side products, and an antagonism arising from the easy degradation of the polymer under mechanical stress as a result of its ether structure and its non-biodegradability, as well as the resulting possible accumulation in the body. These possible side effects will be discussed in this Review and alternative polymers will be evaluated.

Poly(ethylene glycol) in Drug Delivery: Pros and Cons as Well as Potential Alternatives

Current status and future perspectives in atom transfer radical polymerization (ATRP) are presented. Special emphasis is placed on mechanistic understanding of ATRP, recent synthetic and process development, and new controlled polymer architectures enabled by ATRP. New hybrid materials based on organic/inorganic systems and natural/synthetic polymers are presented. Some current and forthcoming applications are described.

Atom Transfer Radical Polymerization (ATRP): Current Status and Future Perspectives

Polystyrene macrocycles have been prepared from ATRP precursors by modification of the terminal bromide to an azide, followed by “click” cyclization with a pendant alkyne from the initiator. This route offers exceptional control over the size and polydispersity of the macrocyclic polymers, as well as providing tolerance to a number of functional groups.

An Efficient Route to Well-Defined Macrocyclic Polymers via “Click” Cyclization

Despite decades of studies devoted to the unique physical properties and potential applications of cyclic polymer topologies, their exploration has remained limited because of synthetic inefficiencies and acyclic impurities. Many recently developed synthetic techniques offer efficient routes to well-defined cyclic macromolecules to answer this need. This tutorial review aims to provide a concise overview of the most significant synthetic contributions in this field, and highlight the relative advantages and disadvantages of each approach.

Synthetic approaches for the preparation of cyclic polymers

Narrow polydisersity cyclic poly(caprolactone) was synthesized by cyclization of linear α,ω-functionalized poly(caprolactone). The linear precursors were prepared via ring-opening polymerization from an azido-functionalized initiator, followed by end group modification to attach a terminal alkyne. Click coupling afforded the cyclic polymer in high yields and provided linear and cyclic poly(caprolactone) with exactly identical molecular weight distributions. The thermal and acid-catalyzed degradation of analogous linear and cyclic poly(caprolactone) samples were investigated to determine the effect of architecture.

Synthesis and Degradation Behavior of Cyclic Poly(ε-caprolactone)

Unlike their more common linear counterparts, cyclic polymers have a ring-like structure and a lack of chain ends. Because of their topology, cyclic polymers exhibit a unique set of properties when compared with linear or branched macromolecules. For example, cyclic homopolymers exhibit a reduced hydrodynamic volume and a slower degradation profile compared with their linear analogues. Cyclic block copolymers self-assemble into compact nanostructures, as illustrated by their reduced domain spacing when cast into thin films and their reduced micellar size in solution. Although methods for preparing well-defined cyclic polymers have only been available since 1980, the extensive utilization of the cyclic topology in nature highlights the vital role that a cyclic architecture can play in imparting valuable physical properties, such as increased chemical stability or propensity towards self-assembly. This Review describes the major developments in the synthesis of cyclic polymers and provides an overview of their fundamental physical properties. In this context, preliminary studies exploring potential applications will be critically assessed and the remaining challenges for the field delineated.

The synthesis, properties and potential applications of cyclic polymers.

The delivery of genetic material to cells offers the potential to treat many genetic diseases. Cationic polymers, specifically poly(ethylene imine) (PEI), are promising gene delivery vectors due to their inherent ability to condense genetic material and successfully affect its transfection. However, PEI and many other cationic polymers also exhibit high cytotoxicity. To systematically study the effect of polymer architecture on gene delivery efficiency and cell cytotoxicity, a set of cyclic PEIs were prepared for the first time and compared to a set of linear PEIs of the exact same molecular weight. Subsequent in vitro transfection studies determined a higher transfection efficiency for each cyclic PEI sample when compared to its linear PEI analogue in addition to reduced toxicity relative to the branched PEI “gold standard” control. These results highlight the critical role that the architecture of PEI can play in both optimizing transfection and reducing cell toxicity.

Scott M. Grayson

Papers

An Efficient Route to Well-Defined Macrocyclic Polymers via “Click” Cyclization

Synthetic approaches for the preparation of cyclic polymers

Synthesis and Degradation Behavior of Cyclic Poly(ε-caprolactone)

The synthesis, properties and potential applications of cyclic polymers.

The Synthesis of Cyclic Poly(ethylene imine) and Exact Linear Analogues: An Evaluation of Gene Delivery Comparing Polymer Architectures.